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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
- B. Brooks, Robert E. Bruccoleri, Barry D. Olafson, D. States, S. Swaminathan, M. Karplus
- 1 June 1983
CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build… Expand
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
- Alexander D. MacKerell, D. Bashford, +26 authors M. Karplus
- Chemistry, Medicine
- The journal of physical chemistry. B
- 14 April 1998
New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance… Expand
CHARMM: The biomolecular simulation program
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. Expand
Evaluation of comparative protein modeling by MODELLER
- A. Sali, L. Potterton, F. Yuan, H. V. van Vlijmen, M. Karplus
- Biology, Medicine
- 1 November 1995
We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, a program for… Expand
Crystallographic R Factor Refinement by Molecular Dynamics
Molecular dynamics was used to refine macromolecular structures by incorporating the difference between the observed crystallographic structure factor amplitude and that calculated from an assumed… Expand
Effective energy function for proteins in solution
A Gaussian solvent‐exclusion model for the solvation free energy is developed. It is based on theoretical considerations and parametrized with experimental data. When combined with the CHARMM 19… Expand
Molecular dynamics simulations of biomolecules
Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. The early view of proteins as relatively rigid… Expand
pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.
A macroscopic electrostatic model is used to calculate the pKa values of the titratable groups in lysozyme. The model makes use of detailed structural information and treats solvation self-energies… Expand
Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.
- B. Brooks, M. Karplus
- Chemistry, Medicine
- Proceedings of the National Academy of Sciences…
- 1 November 1983
A normal mode analysis making use of an empirical potential function including local and nonlocal (nonbonded) interactions is performed for the bovine pancreatic trypsin inhibitor in the full… Expand
CHARMM: The Energy Function and Its Parameterization